Merge branch 'develop' of https://source.jalview.org/git/jalview into features/JAL...

[jalview.git] / src / jalview / io / HtmlFile.java

diff --git a/src/jalview/io/HtmlFile.java b/src/jalview/io/HtmlFile.java
index 73d30dc..af3fb5d 100644 (file)
--- a/src/jalview/io/HtmlFile.java
+++ b/src/jalview/io/HtmlFile.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -22,6 +22,7 @@
 package jalview.io;
 
 import jalview.api.ComplexAlignFile;
+import jalview.api.FeatureSettingsModelI;
 import jalview.api.FeaturesDisplayedI;
 import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.SequenceI;
@@ -59,9 +60,10 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     super(source);
   }
 
-  public HtmlFile(String inFile, String type) throws IOException
+  public HtmlFile(String inFile, DataSourceType sourceType)
+          throws IOException
   {
-    super(inFile, type);
+    super(inFile, sourceType);
   }
 
   @Override
@@ -118,12 +120,13 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
   }
 
   @Override
-  public String print()
+  public String print(SequenceI[] sqs, boolean jvsuffix)
   {
     throw new UnsupportedOperationException(
             "Print method of HtmlFile is not supported!");
   }
 
+  @Override
   public boolean isShowSeqFeatures()
   {
     return showSeqFeatures;
@@ -134,6 +137,7 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     this.showSeqFeatures = showSeqFeatures;
   }
 
+  @Override
   public String getGlobalColourScheme()
   {
     return globalColourScheme;
@@ -144,6 +148,7 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     this.globalColourScheme = globalColourScheme;
   }
 
+  @Override
   public ColumnSelection getColumnSelection()
   {
     return columnSelection;
@@ -154,6 +159,7 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     this.columnSelection = columnSelection;
   }
 
+  @Override
   public SequenceI[] getHiddenSequences()
   {
     return hiddenSequences;
@@ -170,4 +176,19 @@ public class HtmlFile extends AlignFile implements ComplexAlignFile
     return displayedFeatures;
   }
 
+  /**
+   * Returns a descriptor for suitable feature display settings with
+   * <ul>
+   * <li>ResNums or insertions features visible</li>
+   * <li>insertions features coloured red</li>
+   * <li>ResNum features coloured by label</li>
+   * <li>Insertions displayed above (on top of) ResNums</li>
+   * </ul>
+   */
+  @Override
+  public FeatureSettingsModelI getFeatureColourScheme()
+  {
+    return new PDBFeatureSettings();
+  }
+
 }